Journal Article

An integrated cell atlas of the lung in health and disease

Kapellos, Theodore S., Sheppard, Dean, Nawijn, Martijn C., Inecik, Kemal, Collin, Antoine, Huang, Ni, Worlock, Kaylee B., Talavera-López, Carlos, Ramírez-Suástegui, Ciro, Powell, Joseph E., Berg, Marijn, Taylor, Chase J., Travaglini, Kyle J., Desai, Tushar J., Krasnow, Mark A., Xu, Yan, Ibarra, Ignacio L., Zappia, Luke, Dony, Leander, Kole, Tessa M., De Donno, Carlo, Guo, Minzhe, Duong, Thu Elizabeth, Kropski, Jonathan A., Schiller, Herbert B., Chichelnitskiy, Evgeny, Shepherd, Douglas P., Seibold, Max A., Falk, Christine S., Ji, Yuge, Markov, Nikolay S., Apperloo, Leonie, Theis, Fabian J., Sin, Don D., Banchero, Martin, von Papen, Michael, Sikkema, Lisa, Arguel, Marie-Jeanne, Oliver, Amanda J., Leroy, Sylvie, Banovich, Nicholas E., Misharin, Alexander V., Hooshiar Kashani, Baharak, Rajagopal, Jayaraj, Zaragosi, Laure-Emmanuelle, Ansari, Meshal, Pe’er, Dana, Yoshida, Masahiro, Bossé, Yohan, Meyer, Kerstin B., Tata, Purushothama Rao, Gote-Schniering, Janine, Jain, Manu, Barbry, Pascal, Heumos, Lukas, Gay, Aurore C. A., Wilbrey-Clark, Anna, Schultze, Joachim L., Mayr, Christoph H., Kadur Lakshminarasimh

2023

Overview

Single-cell technologies have transformed our understanding of human tissues. Yet, studies typically capture only a limited number of donors and disagree on cell type definitions. Integrating many single-cell datasets can address these limitations of individual studies and capture the variability present in the population. Here we present the integrated Human Lung Cell Atlas (HLCA), combining 49 datasets of the human respiratory system into a single atlas spanning over 2.4 million cells from 486 individuals. The HLCA presents a consensus cell type re-annotation with matching marker genes, including annotations of rare and previously undescribed cell types. Leveraging the number and diversity of individuals in the HLCA, we identify gene modules that are associated with demographic covariates such as age, sex and body mass index, as well as gene modules changing expression along the proximal-to-distal axis of the bronchial tree. Mapping new data to the HLCA enables rapid data annotation and interpretation. Using the HLCA as a reference for the study of disease, we identify shared cell states across multiple lung diseases, including SPP1 + profibrotic monocyte-derived macrophages in COVID-19, pulmonary fibrosis and lung carcinoma. Overall, the HLCA serves as an example for the development and use of large-scale, cross-dataset organ atlases within the Human Cell Atlas. A single-cell atlas of the human lungs, integrating data from 2.4 million cells from 486 individuals and including samples from healthy and diseased lungs, provides a roadmap for the generation of organ-scale cell atlases.

• Publisher: Nature Publishing Group US,Nature Publishing Group
• Subject: 631/114/2397 / 631/114/2401 / 631/337/2019 / 631/80 / 631/80/304 / Annotations / Biomedical and Life Sciences / Biomedicine / Body mass index / Body size / Cancer Research / COVID-19 / Datasets / Fibrosis / Gene expression / Human tissues / Humans / Infectious Diseases / Lung / Lung cancer / Lung carcinoma / Lung diseases / Lung Neoplasms - genetics / Lungs / Macrophages / Metabolic Diseases / Modules / Molecular Medicine / Monocytes / Neurosciences / Pulmonary Fibrosis / Resource / Respiratory system